Speed and accuracy: Having your cake and eating it too

Since the first ab initio methods were developed, the ultimate goal of quantum chemistry has been to provide insights, not readily accessible through experiment, into chemical phenomena. Over the years, two different paths to this end have been taken. The first path provides as accurate a description of relatively small systems as modern computer hardware will allow. The second path follows the desire to perform simulations on systems of physically relevant sizes while sacrificing a certain level of accuracy. The merging of these two paths has allowed for the accurate modeling of large molecular systems through the use of novel theoretical methods. The largest barrier to achieving the goal of accurate calculations on large systems has been the computational requirements of many modern theoretical methods. While these methods are capable of providing the desired level of accuracy, the prohibitive computational requirements can limit system sizes to tens of atoms. By decomposing large chemical systems into more computationally tractable pieces, fragmentation methods have the capability to reduce this barrier and allow for highly accurate descriptions of large molecular systems such as proteins, bulk phase solutions and polymers and nano-scale systems

Geometry Optimizations of Open-Shell Systems with the Fragment Molecular Orbital Method

The ability to perform geometry optimizations on large molecular systems is desirable for both closed- and open-shell species. In this work, the restricted open-shell Hartree–Fock (ROHF) gradients for the fragment molecular orbital (FMO) method are presented. The accuracy of the gradients is tested, and the ability of the method to reproduce adiabatic excitation energies is also investigated. Timing comparisons between the FMO method and full ab initio calculations are also performed, demonstrating the efficiency of the FMO method in modeling large open-shell systems

Open-Shell Formulation of the Fragment Molecular Orbital Method

Performing accurate calculations on large molecular systems is desirable for closed- and open-shell systems. In this work, the fragment molecular orbital method is extended to open-shell systems and implemented in the GAMESS (General Atomic and Molecular Electronic Structure System) program package. The accuracy of the method is tested, and the ability to reproduce reaction enthalpies is demonstrated. These tests also demonstrate its utility in providing an efficient means to model large open-shell systems

Fragmentation Methods: A Route to Accurate Calculations on Large Systems

Theoretical chemists have always strived to perform quantum mechanics (QM) calculations on larger and larger molecules and molecular systems, as well as condensed phase species, that are frequently much larger than the current state-of-the-art would suggest is possible. The desire to study species (with acceptable accuracy) that are larger than appears to be feasible has naturally led to the development of novel methods, including semiempirical approaches, reduced scaling methods, and fragmentation methods. The focus of the present review is on fragmentation methods, in which a large molecule or molecular system is made more computationally tractable by explicitly considering only one part (fragment) of the whole in any particular calculation. If one can divide a species of interest into fragments, employ some level of ab initio QM to calculate the wave function, energy, and properties of each fragment, and then combine the results from the fragment calculations to predict the same properties for the whole, the possibility exists that the accuracy of the outcome can approach that which would be obtained from a full (nonfragmented) calculation. It is this goal that drives the development of fragmentation methods

Fully Integrated Effective Fragment Molecular Orbital Method

In this work, the effective fragment potential (EFP) method is fully integrated (FI) into the fragment molecular orbital (FMO) method to produce an effective fragment molecular orbital (EFMO) method that is able to account for all of the fundamental types of both bonded and intermolecular interactions, including many-body effects, in an accurate and efficient manner. The accuracy of the method is tested and compared to both the standard FMO method as well as to fully ab initio methods. It is shown that the FIEFMO method provides significant reductions in error while at the same time reducing the computational cost associated with standard FMO calculations by up to 96%

Systematic Fragmentation Method and the Effective Fragment Potential: An Efficient Method for Capturing Molecular Energies

The systematic fragmentation method fragments a large molecular system into smaller pieces, in such a way as to greatly reduce the computational cost while retaining nearly the accuracy of the parent ab initio electronic structure method. In order to attain the desired (sub-kcal/mol) accuracy, one must properly account for the nonbonded interactions between the separated fragments. Since, for a large molecular species, there can be a great many fragments and therefore a great many nonbonded interactions, computations of the nonbonded interactions can be very time-consuming. The present work explores the efficacy of employing the effective fragment potential (EFP) method to obtain the nonbonded interactions since the EFP method has been shown previously to capture nonbonded interactions with an accuracy that is often comparable to that of second-order perturbation theory. It is demonstrated that for nonbonded interactions that are not high on the repulsive wall (generally \u3e2.7 Å), the EFP method appears to be a viable approach for evaluating the nonbonded interactions. The efficacy of the EFP method for this purpose is illustrated by comparing the method to ab initio methods for small water clusters, the ZOVGAS molecule, retinal, and the α-helix. Using SFM with EFP for nonbonded interactions yields an error of 0.2 kcal/mol for the retinal cis−trans isomerization and a mean error of 1.0 kcal/mol for the isomerization energies of five small (120−170 atoms) α-helices

Accurate Methods for Large Molecular Systems

Three exciting new methods that address the accurate prediction of processes and properties of large molecular systems are discussed. The systematic fragmentation method (SFM) and the fragment molecular orbital (FMO) method both decompose a large molecular system (e.g., protein, liquid, zeolite) into small subunits (fragments) in very different ways that are designed to both retain the high accuracy of the chosen quantum mechanical level of theory while greatly reducing the demands on computational time and resources. Each of these methods is inherently scalable and is therefore eminently capable of taking advantage of massively parallel computer hardware while retaining the accuracy of the corresponding electronic structure method from which it is derived. The effective fragment potential (EFP) method is a sophisticated approach for the prediction of nonbonded and intermolecular interactions. Therefore, the EFP method provides a way to further reduce the computational effort while retaining accuracy by treating the far-field interactions in place of the full electronic structure method. The performance of the methods is demonstrated using applications to several systems, including benzene dimer, small organic species, pieces of the α helix, water, and ionic liquids

Racial and ethnic disparities in cervical cancer screening from three U.S. healthcare settings

INTRODUCTION: This study sought to characterize racial and ethnic disparities in cervical cancer screening and follow-up of abnormal findings across 3 U.S. healthcare settings. METHODS: Data were from 2016 to 2019 and were analyzed in 2022, reflecting sites within the Multi-level Optimization of the Cervical Cancer Screening Process in Diverse Settings & Populations Research Center, part of the Population-based Research to Optimize the Screening Process consortium, including a safety-net system in the southwestern U.S., a northwestern mixed-model system, and a northeastern integrated healthcare system. Screening uptake was evaluated among average-risk patients (i.e., no previous abnormalities) by race and ethnicity as captured in the electronic health record, using chi-square tests. Among patients with abnormal findings requiring follow-up, the proportion receiving colposcopy or biopsy within 6 months was reported. Multivariable regression was conducted to assess how clinical, socioeconomic, and structural characteristics mediate observed differences. RESULTS: Among 188,415 eligible patients, 62.8% received cervical cancer screening during the 3-year study period. Screening use was lower among non-Hispanic Black patients (53.2%) and higher among Hispanic (65.4%,) and Asian/Pacific Islander (66.5%) than among non-Hispanic White patients (63.5%, all p\u3c0.001). Most differences were explained by the distribution of patients across sites and differences in insurance. Hispanic patients remained more likely to screen after controlling for a variety of clinical and sociodemographic factors (risk ratio=1.14, CI=1.12, 1.16). Among those receiving any screening test, Black and Hispanic patients were more likely to receive Pap-only testing (versus receiving co-testing). Follow-up from abnormal results was low for all groups (72.5%) but highest among Hispanic participants (78.8%, p\u3c0.001). CONCLUSIONS: In a large cohort receiving care across 3 diverse healthcare settings, cervical cancer screening and follow-up were below 80% coverage targets. Lower screening for Black patients was attenuated by controlling for insurance and site of care, underscoring the role of systemic inequity. In addition, it is crucial to improve follow-up after abnormalities are identified, which was low for all populations

Surface Affinity of the Hydronium Ion: The Effective Fragment Potential and Umbrella Sampling

The surface affinity of the hydronium ion in water is investigated with umbrella sampling and classical molecular dynamics simulations, in which the system is described with the effective fragment potential (EFP). The solvated hydronium ion is also explored using second order perturbation theory for the hydronium ion and the empirical TIP5P potential for the waters. Umbrella sampling is used to analyze the surface affinity of the hydronium ion, varying the number of solvent water molecules from 32 to 256. Umbrella sampling with the EFP method predicts the hydronium ion to most probably lie about halfway between the center and edge of the water cluster, independent of the cluster size. Umbrella sampling using MP2 for the hydronium ion and TIP5P for the solvating waters predicts that the solvated proton most probably lies about 0.5–2.0 Å from the edge of the water cluster independent of the cluster size